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Multispecies models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams
Molecular Ecology ( IF 4.9 ) Pub Date : 2020-09-23 , DOI: 10.1111/mec.15644
Emily F McColl-Gausden 1 , Andrew R Weeks 1, 2 , Rhys A Coleman 3 , Katie L Robinson 1 , Sue Song 2 , Tarmo A Raadik 4 , Reid Tingley 5
Affiliation  

Environmental DNA (eDNA) sampling can provide accurate, cost-effective, landscape-level data on species distributions. Previous studies have compared the sensitivity of eDNA sampling to traditional sampling methods for single species, but similar comparative studies on multispecies eDNA metabarcoding are rare. Using hierarchical site occupancy detection models, we examined whether key choices associated with eDNA metabarcoding (primer selection, low-abundance read filtering and the number of positive water samples used to classify a species as present at a site) affect the sensitivity of metabarcoding, relative to backpack electrofishing for fish in freshwater streams. Under all scenarios (teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering thresholds; one or two positive samples required to classify species as present), we found that eDNA metabarcoding is, on average, more sensitive than electrofishing. Combining vertebrate and teleostei markers resulted in higher detection probabilities relative to the use of either marker in isolation. Increasing the threshold used to filter low-abundance reads decreased species detection probabilities but did not change our overall finding that eDNA metabarcoding was more sensitive than electrofishing. Using a threshold of two positive water samples (out of five) to classify a species as present typically had negligible effects on detection probabilities compared to using one positive water sample. Our findings demonstrate that eDNA metabarcoding is generally more sensitive than electrofishing for conducting fish surveys in freshwater streams, and that this outcome is not sensitive to methodological decisions associated with metabarcoding.

中文翻译:

多物种模型显示,在淡水溪流中进行鱼类调查时,eDNA 元条形码比背包式电捕鱼更敏感

环境 DNA (eDNA) 采样可以提供关于物种分布的准确、具有成本效益的景观级数据。以前的研究比较了 eDNA 采样与传统采样方法对单一物种的敏感性,但对多物种 eDNA 元条形码的类似比较研究很少见。使用分层站点占用检测模型,我们检查了与 eDNA 元条形码相关的关键选择(引物选择、低丰度读取过滤和用于将物种分类为存在于站点的阳性水样的数量)是否影响元条形码的灵敏度、相对为淡水溪流中的鱼类背负电捕鱼。在所有情况下(硬骨鱼和脊椎动物引物;0%、0.1% 和 1% 读取过滤阈值;将物种分类为存在所需的一两个阳性样本),我们发现,平均而言,eDNA 元条形码比电捕鱼更敏感。与单独使用任一标记相比,将脊椎动物和硬骨动物标记相结合导致更高的检测概率。增加用于过滤低丰度读数的阈值会降低物种检测概率,但并没有改变我们的总体发现,即 eDNA 元条形码比电捕鱼更敏感。与使用一个阳性水样相比,使用两个阳性水样(五分之一)的阈值对存在的物种进行分类通常对检测概率的影响可以忽略不计。我们的研究结果表明,在淡水溪流中进行鱼类调查时,eDNA 元条形码通常比电捕鱼更敏感,
更新日期:2020-09-23
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